Concept 19 The DNA molecule is shaped like a twisted ladder.
James Watson and Francis Crick explain how they solved the structure of DNA. Erwin Chargaff explain how he measured the levels of each of the four nitrogenous bases.
I'm James Watson. I'm Francis Crick. In 1953, Francis and I published the first accurate model of the DNA molecule. We were interested in DNA — the hereditary molecule of life. We wanted to build on what was chemically known about DNA, and determine its actual structure. For example, Phoebus Levene had shown that each nucleotide building block of DNA is made up of a phosphate group linked to a deoxyribose sugar — which, in turn, is linked to one of four nitrogenous bases — adenine (A), guanine (G), cytosine (C), and thymine (T). Nucleotides are linked in a series — from one phosphate, to the next sugar, to the next phosphate, and so on. Although Levene had proposed the correct chemical linkages, his tetranucleotide theory was wrong. If DNA had a fixed, repetitive sequence, it wouldn't be intelligent enough to carry any information. And after Oswald Avery's landmark paper, we knew that DNA had to be intelligent. In fact, it made more sense if the order of the nucleotides changed. Information can then be coded into the DNA sequence. DNA, not protein, was the Rosetta Stone for unraveling the true secret of life. I'm Erwin Chargaff. I also thought there had to be more to DNA than just simple repetitive tetranucleotide blocks. I isolated DNA from different organisms and measured the levels of each of the four nitrogenous bases. Here are my results. As you can see, the amount of adenine is very close to the amount of thymine. And there is just as much guanine as there is cytosine. If Levene's tetranucleotide theory was correct, then the amounts of A, T, G and C would be the same in the DNA of all organisms. This is clearly not the case. Instead, the nucleotides must be arranged so that there are about equal amounts of A and T, and about equal amounts of G and C. However, I wasn't able to make sense of these striking, but perhaps meaningless, regularities. As you'll see, Chargaff's base ratios were an important clue in our work on the DNA structure. At about the same time, Linus Pauling at Cal Tech used his knowledge of chemistry and a powerful new technique called X-ray crystallography to discover a corkscrew-shaped structure found in many proteins — the alpha-helix. Francis and I followed Pauling's approach of using chemistry and X-ray diffraction patterns to solve the structure of DNA. X-ray diffraction patterns can provide a lot of information about the shape and structure of a molecule. If a stream of X-rays is directed at a crystallized substance, some rays are diffracted, or scattered, as they encounter the atoms. The scattered X-rays then interfere with each other and produce spots of different intensities and these can be recorded on photographic film. The resulting diffraction pattern is a unique "signature" of the molecule. At the time, DNA couldn't be crystallized but we could get two different types of DNA fibers. These fibers gave two distinct diffraction patterns. Rosalind Franklin and Maurice Wilkins made these DNA X-ray diffraction patterns. I concentrated on the X-ray data from this form of DNA. As you can see there are a lot more spots on it and therefore more information. I was able to calculate the basic dimensions of the DNA molecule. While Rosalind was working on the other X-ray crystallograph, Francis was immediately struck by the symmetry of simplicity of this X-ray pattern. It was clear to me that all the information we needed was here in this X-ray pattern. The distinctive "X" in this X-ray photo is the telltale pattern of a helix. Because the X-ray pattern is so regular, the dimensions of the helix must also be consistent. For example, the diameter of the helix stays the same. In an X-ray diffraction pattern, the closer the spots, the larger the actual distance. So the horizontal bars actually correspond to helical turns. The vertical distance between the bars — 34 Angstroms — is a measure of the height of one helical turn. The distance from the middle of the X-ray pattern to the top is measurable at 3.4 angstroms. This corresponds to the distance between two stacked base pairs. Since, we know the height of one helical repeat — 34 angstroms — and we know the distance between stacked base pairs — 3.4 angstroms — there must be 10 nucleotides per helical repeat. The helix's pitch, or its degree of rise, can be calculated from the angle the "X" makes with the horizontal axis. If we distort the helix, you can get an idea how the helical pitch is related to the X-ray pattern. From this X-ray diffraction pattern, I deduced that DNA should be a double helix with the phosphate groups on the outside and the bases on the inside. And from the measurements made by Franklin and Wilkins, we knew the basic dimensions of the helix. Jim and I were eager to fit everything known about DNA into an accurate model. But questions still remained: How do the helices fit together? How are the nitrogen bases arranged? It was a race to solve the DNA structure. We knew that after solving the alpha-helix structure in proteins, Linus Pauling was interested in DNA structure. Just as we were beginning to build tentative DNA models, we heard that Pauling had submitted a paper on the structure for DNA. We waited on pins and needles to review his scheme, which turned out to be a triple helix. Everyone agreed that this model couldn't be right. Pauling put the phosphate groups in the core of each helix with the nitrogenous bases facing out. Three such helices then intertwined to make one DNA molecule. Pauling had forgotten the negative charges of the oxygen atom in each phosphate group. Facing toward the middle, and stacked on top of each other, these charges would repel one another, making it impossible for the molecule to hold together. Almost unbelievably, the man who had written the book on the chemical bond got it wrong. Linus' mistake encouraged us to work even harder, for we knew he would redouble his efforts to set his error right. One day, not long after his paper came out, I began to play with paper cutouts of the nitrogen bases. I knew that nucleotides could pair and form weak bonds called "hydrogen bonds." Unlike the strong "covalent" bonds that join phosphate, sugar, and base into a nucleotide, hydrogen bonds are formed when nitrogen or oxygen shares a hydrogen atom. I started pairing nucleotides based on possible hydrogen bonds. I compared the width of different hydrogen bond pairs. Some pairs were obviously different in width. If these pairs really occurred in the DNA helix, then the helix would be uneven and would bulge in and out. In a moment of part insight and part luck, I realized that adenine could pair closely with thymine, and that guanine could pair closely with cytosine. Moreover, the A/T base pair was about the same width as a G/C base pair. This "base pairing" agreed with Chargaff's ratios, and allowed the bases to compactly stack on top of one another. Guanine makes 3 hydrogen bonds with cytosine, and adenine makes 2 hydrogen bonds with thymine. I became convinced that base pairing was the key to DNA's structure. Francis agreed with me. He also pointed out that because of certain bond angles and the proximity of the base pairs, the two helices had to run in opposite directions. The helices are antiparallel to one another. Using metal scraps from the machine shop, Francis and I built a 3-dimensional model of DNA. This six-foot model incorporated what was already known with my A/T and G/C base pairing scheme and Francis' idea of antiparallel strands. Everything clicked into place beautifully. Upon looking at our model, everyone — including Maurice and Rosalind — agreed that we had the right DNA structure. So, DNA is like a twisted ladder, where the sugar and phosphate are the rails, and the base pairs are the rungs. The rails run in opposite orientation to each other. The nucleotide rungs are complementary to each other. Wherever there is an A on one strand, there is a T in the same position on the other strand. Similarly, wherever there is a G on one strand, there is a C in the same position on the other strand. Francis and I were so excited by our beautiful model that we quickly wrote up the results and submitted the 900-word paper to the scientific journal Nature. In the paper, we concluded: It hasn't escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material. Maurice and Rosalind published their findings in separate papers following ours.
While visiting Cambridge in 1952, Erwin Chargaff met Watson and Crick. Chargaff was not impressed with the duo, especially after Crick admitted to not knowing the chemical structures of the nitrogen bases.
Watson and Crick ended their 1953 paper by saying that the base pairing in their DNA helix model "suggests a possible copying mechanism for genetic material." What would this mechanism be?